Non-coding RNAs binding to the nucleoid protein HU in Escherichia

23 24 Some unidentified RNA molecules, together with the nucleoid protein HU, were 25 suggested to be involved in the nucleoid structure of Escherichia coli. HU is a conserved 26 protein known for its role in binding to DNA and maintaining negative supercoils in the 27 latter. HU also binds to a few RNAs but the full spectrum of its binding targets in the cell 28 is not known. To understand any interaction of HU with RNA in the nucleoid structure, 29 we immunoprecipitated potential HU-RNA complexes from cells and examined bound 30 RNAs by hybridization to whole-genome tiling arrays. We identified associations 31 between HU and ten new intragenic and intergenic noncoding (nc) RNAs, two of which 32 are homologous to the annotated Bacterial Interspersed Mosaic Elements (BIME) and 33 boxC DNA repeat elements. We confirmed direct binding of HU to BIME RNA in vitro. 34 We also studied the nucleoid shape of HU and two of the ncRNA mutants (nc1 and nc5) 35 by transmission electron microscopy and showed that both HU and the two ncRNAs play 36 a role in nucleoid morphology. We propose that at least two of the ncRNA species 37 complex with HU and help the formation or maintenance of the architecture of the E. coli 38 chromosome. We also observed binding of HU with rRNA and tRNA segments, a few 39 sRNAs and a distinct small set of mRNAs although significance, if any, of these 40 associations is not known. 41 42